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Isophthalate dioxygenase in complex with isophthalate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 ammonium fluoride 0.2 M, PEG 3350 20%, 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 5.29 76.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.956 α = 90 b = 146.956 β = 90 c = 146.956 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-6000HE 2022-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.3 25.22 98.7 0.965 9.9 3.7 15945
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.57 0.935 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.3 25.22 15342 772 99.59 0.17652 0.17456 0.1811 0.21764 0.2258 RANDOM 67.196
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.959 r_long_range_B_refined 14.51 r_long_range_B_other 14.509 r_scangle_other 11.671 r_mcangle_it 10.256 r_mcangle_other 10.256 r_dihedral_angle_2_deg 10.218 r_dihedral_angle_1_deg 7.989 r_scbond_it 7.519 r_scbond_other 7.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.959 r_long_range_B_refined 14.51 r_long_range_B_other 14.509 r_scangle_other 11.671 r_mcangle_it 10.256 r_mcangle_other 10.256 r_dihedral_angle_2_deg 10.218 r_dihedral_angle_1_deg 7.989 r_scbond_it 7.519 r_scbond_other 7.517 r_mcbond_it 6.586 r_mcbond_other 6.578 r_angle_refined_deg 1.958 r_angle_other_deg 0.647 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3467 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing